Rune Nilsen grew up in Hamar and played in the youth team of the Hamar team Flygemais from the age of 15. He had then shown himself to be a rare and fast striker who scored a lot of goals. On 10th of June 2005 (season 15), as a 17-year-old, he was finally accepted into the Flygemais first team. However, it did not take long before German scouts who had been following him for a long time signaled interest. Three days later, Nilsen was bought for NOK 2,150,000 by the German scouts and their FC Wunderbar. ​

After only five days at his new German club, Nilsen was included in the squad for the first team's league match in the German seventh division, however without making an appearance. Two days later, he finally got a try out for the reserve team. The match ended with a 0-7 loss and Nilsen also received a yellow card one minute before the end after a very ugly foul. After this, Nilsen was used in four reserve team matches and managed to show some of his qualities by scoring four goals and a hat-trick. The praise was great, and he was again included in the first-team squad, but unfortunately he was not used this time either. On 20th of July 2005, Nilsen played his last match for F.C Wunderbar. A short career of just over one month was enough to not settle in Germany. Still, plenty of interested clubs queed up to secure the youngster's contract and when the Kongsvinger team Torden FK put an amount of NOK 6.5 million on the table, it was an easy choice for Rune. In retrospect, it has emerged that although this was a large amount for the Germans, it was also a very bitter decision for them, to let go of their self-discovered "diamond".